This paper presents models for simulating the operation of a polymer electrolyte membrane fuel cell (PEMFC) system and the results of the dynamic simulations. The entire system included a PEMFC stack and balance-of-plant components such as an air supply blower, a membrane humidifier, a fuel supply unit, and a heat management unit. Mathematical modeling for the computation of power generation and heat transfer of the PEMFC stack, the heat and mass transfer of the humidifier, and the energy transfer of the cooling system was set up. Theoretical and experiential data such as the voltage-current density relationship of the cell stack and the performance maps of blowers and pumps, together with semi-theoretical heat and mass transfer equations, were used to represent the characteristics of all the components. The effect of the thermal inertia of solid parts was considered in the fuel cell stack, the membrane humidifier, and the radiator. System dynamic behaviors under various operating conditions due to changes in stack current and ambient temperature were predicted. The sudden abnormal operations of the cooling water circulation pump and the radiator fan were also simulated as an example of component malfunctions.